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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ), 'gf_id' => 'HOM05D001299', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001299' ), 'data_identifier' => 'HOM05D001299', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001299', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '484', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p17170' => 'bna', 'A02p31870' => 'bna', 'A06p44510' => 'bna', 'A06p47140' => 'bna', 'Aa31LG1G90' => 'aar', 'Aa31LG2G8620' => 'aar', 'Aa31LG4G9970' => 'aar', 'Aa31LG5G15190' => 'aar', 'Aa31LG9G8690' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3784' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4077' => 'aag', 'Actinidia05772' => 'ach', 'Actinidia15245' => 'ach', 'Actinidia30936' => 'ach', 'Actinidia32353' => 'ach', 'Actinidia36687' => 'ach', 'Ah.06g189080' => 'amhyb', 'Ah.06g192220' => 'amhyb', 'AL2G30680' => 'aly', 'AL3G14950' => 'aly', 'AL5G10250' => 'aly', 'AL8G15300' => 'aly', 'Aqoxy2G00426' => 'aox', 'Aqoxy2G03452' => 'aox', 'Aqoxy3G03977' => 'aox', 'Aqoxy7G02972' => 'aox', 'arahy.Tifrunner.gnm1.ann1.38UHBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.403SR1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6RWY33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6YEN7W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.85QD0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D99XSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IMCF17' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NFPE2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZN1LAP' => 'arhy', 'AT1G71100' => 'ath', 'AT2G01290' => 'ath', 'AT3G04790' => 'ath', 'AT5G44520' => 'ath', 'ATR0326G046' => 'atr', 'ATR0665G255' => 'atr', 'ATR0763G220' => 'atr', 'ATR1096G013' => 'atr', 'ATR1098G024' => 'atr', 'Atru.chr10.662' => 'acertr', 'Atru.chr11.382' => 'acertr', 'Atru.chr2.797' => 'acertr', 'AUR62000706' => 'cqu', 'AUR62001026' => 'cqu', 'AUR62004926' => 'cqu', 'AUR62005257' => 'cqu', 'BcaB02g06566' => 'bca', 'BcaB04g21346' => 'bca', 'BcaB05g24644' => 'bca', 'BcaB07g30410' => 'bca', 'BcaC03g15267' => 'bca', 'BcaC03g17020' => 'bca', 'BcaC06g31318' => 'bca', 'BcaC06g31319' => 'bca', 'BcaC06g31322' => 'bca', 'BcaC06g31610' => 'bca', 'BcaC06g34198' => 'bca', 'BcaC06g34201' => 'bca', 'BcaC06g34203' => 'bca', 'BcaC06g34545' => 'bca', 'BcaNung06423' => 'bca', 'BcaNung06425' => 'bca', 'BolC2t08905H' => 'bol', 'BolC2t11018H' => 'bol', 'BolC5t34903H' => 'bol', 'BolC7t43265H' => 'bol', 'BolC7t43711H' => 'bol', 'BraA01t04504Z' => 'bra', 'BraA02t06763Z' => 'bra', 'BraA02t08196Z' => 'bra', 'BraA05t22975Z' => 'bra', 'BraA06t27325Z' => 'bra', 'BraA06t27586Z' => 'bra', 'C02p28610' => 'bna', 'C02p49310' => 'bna', 'C07p27350' => 'bna', 'C07p31720' => 'bna', 'CAN.G134.110' => 'can', 'CAN.G15.12' => 'can', 'CAN.G15.13' => 'can', 'CAN.G1693.12' => 'can', 'CAN.G359.9' => 'can', 'CAN.G637.61' => 'can', 'CAN.G675.34' => 'can', 'CAN.G978.2' => 'can', 'CAN.G99.4' => 'can', 'CANSAT01G0158' => 'cansat', 'CANSAT01G1020' => 'cansat', 'CANSAT35G1957' => 'cansat', 'CANSAT54G2431' => 'cansat', 'CARHR064390' => 'chi', 'CARHR079040' => 'chi', 'CARHR143820' => 'chi', 'CARHR178590' => 'chi', 'Carub.0002s1792' => 'cru', 'Carub.0003s0396' => 'cru', 'Carub.0005s0027' => 'cru', 'Carub.0008s0398' => 'cru', 'Ca_00935_v3' => 'car', 'Ca_09414_v3' => 'car', 'Ca_11097_v3' => 'car', 'CBR_g28662' => 'cbr', 'CBR_g39237' => 'cbr', 'CBR_g50124' => 'cbr', 'Cc01_g03210' => 'ccan', 'Cc01_g03230' => 'ccan', 'Cc09_g07140' => 'ccan', 'Cc11_g08950' => 'ccan', 'CDE03G0248' => 'cde', 'CDE04G0264' => 'cde', 'CDE06G2654' => 'cde', 'CDE07G1771' => 'cde', 'CDE10G0303' => 'cde', 'CDE10G0370' => 'cde', 'CDE10G0413' => 'cde', 'CDE10G0779' => 'cde', 'Cfa000759' => 'cfa', 'Cfa006447' => 'cfa', 'Cfa008579' => 'cfa', 'Cfa025542' => 'cfa', 'Ciclev10002135m.g' => 'ccl', 'Ciclev10010606m.g' => 'ccl', 'Ciclev10015984m.g' => 'ccl', 'Ciclev10016309m.g' => 'ccl', 'CiPaw.05G247800' => 'cil', 'CiPaw.06G013500' => 'cil', 'CiPaw.07G065400' => 'cil', 'CiPaw.10G111000' => 'cil', 'ClCG01G006170' => 'cla', 'ClCG01G008880' => 'cla', 'ClCG02G016530' => 'cla', 'ClCG05G022210' => 'cla', 'COL.COLO4_15308' => 'col', 'COL.COLO4_20452' => 'col', 'COL.COLO4_26895' => 'col', 'COL.COLO4_35738' => 'col', 'Cpa.g.c33583' => 'cpa', 'Cpa.g.sc117.78' => 'cpa', 'Cpa.g.sc285.1' => 'cpa', 'Cpa.g.sc65.113' => 'cpa', 'Cre03.g187450' => 'cre', 'Cre07.g314600' => 'cre', 'CsaV3_1G037750' => 'csa', 'CsaV3_2G004240' => 'csa', 'CsaV3_5G028490' => 'csa', 'CsaV3_5G034910' => 'csa', 'CSS0000531' => 'camsi', 'CSS0007044' => 'camsi', 'CSS0007807' => 'camsi', 'CSS0007995' => 'camsi', 'CSS0009698' => 'camsi', 'CSS0011897' => 'camsi', 'CSS0019604' => 'camsi', 'CSS0021335' => 'camsi', 'CSS0023575' => 'camsi', 'CSS0024772' => 'camsi', 'CSS0034631' => 'camsi', 'CSS0046492' => 'camsi', 'DCAR_007280' => 'dca', 'DCAR_011702' => 'dca', 'DCAR_026764' => 'dca', 'Dinv04803' => 'din', 'Dinv05146' => 'din', 'Dinv05368' => 'din', 'Dinv05888' => 'din', 'Dinv16199' => 'din', 'Duzib106G1319' => 'dzi', 'Duzib177G0313' => 'dzi', 'Duzib235G0189' => 'dzi', 'Duzib248G0506' => 'dzi', 'Duzib251G0712' => 'dzi', 'Duzib268G0091' => 'dzi', 'ECA232G0896' => 'eca', 'ECA232G3192' => 'eca', 'ECA233G2989' => 'eca', 'ECA233G3687' => 'eca', 'ECA247G3420' => 'eca', 'EL10Ac4g09113' => 'bvu', 'EL10Ac4g09844' => 'bvu', 'EL10Ac8g19624' => 'bvu', 'Eucgr.B02112' => 'egr', 'Eucgr.D01028' => 'egr', 'Eucgr.G02204' => 'egr', 'Eucgr.H04380' => 'egr', 'Eucgr.L03383' => 'egr', 'FAN02G4386' => 'fan', 'FAN05G3118' => 'fan', 'FAN05G5636' => 'fan', 'FAN07G2528' => 'fan', 'FAN09G0985' => 'fan', 'FAN09G2166' => 'fan', 'FAN12G3350' => 'fan', 'FAN14G1011' => 'fan', 'FAN16G0158' => 'fan', 'FAN17G1336' => 'fan', 'FAN19G1625' => 'fan', 'FAN21G1530' => 'fan', 'FAN22G0149' => 'fan', 'FAN23G2297' => 'fan', 'FAN25G0007' => 'fan', 'FAN26G3398' => 'fan', 'FAN28G2053' => 'fan', 'FvH4_1g20420' => 'fve', 'FvH4_3g11560' => 'fve', 'FvH4_4g32160' => 'fve', 'FvH4_6g03160' => 'fve', 'Glyma.03G246300' => 'gma', 'Glyma.08G214700' => 'gma', 'Glyma.09G030500' => 'gma', 'Glyma.10G265400' => 'gma', 'Glyma.15G136200' => 'gma', 'Glyma.19G243800' => 'gma', 'Glyma.20G125200' => 'gma', 'Gohir.A01G153700' => 'ghi', 'Gohir.A03G123200' => 'ghi', 'Gohir.A06G118100' => 'ghi', 'Gohir.A08G214500' => 'ghi', 'Gohir.A11G253800' => 'ghi', 'Gohir.A12G150100' => 'ghi', 'Gohir.D01G100100' => 'ghi', 'Gohir.D02G145800' => 'ghi', 'Gohir.D06G121900' => 'ghi', 'Gohir.D08G231700' => 'ghi', 'Gohir.D11G263700' => 'ghi', 'Gohir.D12G153700' => 'ghi', 'Gorai.002G181100' => 'gra', 'Gorai.004G246100' => 'gra', 'Gorai.005G163200' => 'gra', 'Gorai.007G283700' => 'gra', 'Gorai.008G166200' => 'gra', 'Gorai.010G142100' => 'gra', 'GSVIVG01021828001' => 'vvi', 'GSVIVG01025127001' => 'vvi', 'GSVIVG01037941001' => 'vvi', 'HanXRQChr08g0212591' => 'han', 'HanXRQChr11g0341271' => 'han', 'HanXRQChr12g0366161' => 'han', 'HanXRQChr15g0477321' => 'han', 'HanXRQChr15g0488591' => 'han', 'Haze_04346' => 'cav', 'Haze_05959' => 'cav', 'Haze_11034' => 'cav', 'Haze_27613' => 'cav', 'Hma1.2p1_0079F.1_g041120' => 'hma', 'Hma1.2p1_0079F.1_g041140' => 'hma', 'Hma1.2p1_0114F.1_g055180' => 'hma', 'HPP92_000971' => 'vpl', 'HPP92_001009' => 'vpl', 'HPP92_017648' => 'vpl', 'HPP92_027368' => 'vpl', 'Hund06960' => 'sun', 'Lalb_Chr02g0145531' => 'lal', 'Lalb_Chr06g0165631' => 'lal', 'Lalb_Chr15g0076831' => 'lal', 'Lalb_Chr15g0089001' => 'lal', 'Lalb_Chr21g0308501' => 'lal', 'Lj1A1156T42' => 'lonja', 'Lj1g0018965' => 'lja', 'Lj3P875T18' => 'lonja', 'Lj5g0026699' => 'lja', 'Lj6g0006807' => 'lja', 'Lj6g0028150' => 'lja', 'Lj6P749T27' => 'lonja', 'Lj7A580T62' => 'lonja', 'Lsat_1_v5_gn_1_130040' => 'lsa', 'Lsat_1_v5_gn_3_54301' => 'lsa', 'Lsat_1_v5_gn_4_165321' => 'lsa', 'Lsat_1_v5_gn_8_34821' => 'lsa', 'Lsat_1_v5_gn_8_43001' => 'lsa', 'Manes.02G135000' => 'mes', 'Manes.03G067266' => 'mes', 'Manes.06G061700' => 'mes', 'Manes.08G132900' => 'mes', 'Manes.09G154000' => 'mes', 'Manes.14G135500' => 'mes', 'Mapoly0109s0045' => 'mpo', 'Mapoly0213s0005' => 'mpo', 'MBI05_g12590_MAGBIO' => 'mbi', 'MBI10_g20067_MAGBIO' => 'mbi', 'MBI18_g14310_MAGBIO' => 'mbi', 'MBI18_g26477_MAGBIO' => 'mbi', 'MBI19_g24362_MAGBIO' => 'mbi', 'MCO05G574' => 'mco', 'MCO09G104' => 'mco', 'MD04G1222500' => 'mdo', 'MD10G1240700' => 'mdo', 'MD12G1238600' => 'mdo', 'MD13G1028000' => 'mdo', 'MD16G1030900' => 'mdo', 'Medtr1g108440' => 'mtr', 'Medtr2g032540' => 'mtr', 'Medtr7g114900' => 'mtr', 'MELO3C004370.2' => 'cme', 'MELO3C005310.2' => 'cme', 'MELO3C012301.2' => 'cme', 'MELO3C021811.2' => 'cme', 'Migut.E00408' => 'egut', 'Migut.L00759' => 'egut', 'Migut.M01940' => 'egut', 'Migut.N03150' => 'egut', 'MSTRG.13572' => 'ama', 'MSTRG.16317' => 'ama', 'MSTRG.2189' => 'ama', 'Nitab4.5_0000414g0100' => 'nta', 'Nitab4.5_0004469g0070' => 'nta', 'Nitab4.5_0005582g0010' => 'nta', 'Nitab4.5_0006134g0010' => 'nta', 'Nitab4.5_0007384g0010' => 'nta', 'Nitab4.5_0007613g0040' => 'nta', 'Nitab4.5_0010415g0020' => 'nta', 'Nitab4.5_0012569g0010' => 'nta', 'Nn1g02426' => 'nnu', 'Nn4g24066' => 'nnu', 'Nn7g36808' => 'nnu', 'Nn7g37865' => 'nnu', 'Oeu002659.5' => 'oeu', 'Oeu027463.2' => 'oeu', 'Oeu044335.1' => 'oeu', 'Oeu063345.2' => 'oeu', 'Os03g0781400' => 'osa', 'Os04g0306400' => 'osa', 'Os07g0176900' => 'osa', 'Peaxi162Scf00119g00159' => 'pax', 'Peaxi162Scf00195g00521' => 'pax', 'Peaxi162Scf00205g00053' => 'pax', 'Peaxi162Scf00282g00110' => 'pax', 'PGR004G1834' => 'pgr', 'PGR119G2516' => 'pgr', 'PGSC0003DMG400005961' => 'stu', 'PGSC0003DMG400019448' => 'stu', 'PGSC0003DMG400021135' => 'stu', 'PGSC0003DMG400030509' => 'stu', 'Phvul.002G234600' => 'pvu', 'Phvul.006G100600' => 'pvu', 'Phvul.006G122300' => 'pvu', 'Phvul.007G036500' => 'pvu', 'Potri.001G225700' => 'ptr', 'Potri.005G052000' => 'ptr', 'Potri.006G039700' => 'ptr', 'Potri.006G039800' => 'ptr', 'Potri.008G127600' => 'ptr', 'Potri.010G115300' => 'ptr', 'Potri.011G155500' => 'ptr', 'Potri.013G039400' => 'ptr', 'Pp3c16_10280' => 'ppa', 'Pp3c16_13350' => 'ppa', 'Pp3c19_7350' => 'ppa', 'Pp3c1_400' => 'ppa', 'Pp3c5_21490' => 'ppa', 'Pp3c5_830' => 'ppa', 'PRCOL_00001287' => 'pco', 'PRCOL_00006791' => 'pco', 'Prupe.1G322200' => 'ppe', 'Prupe.4G102900' => 'ppe', 'Prupe.6G341500' => 'ppe', 'Psat1g163720' => 'psa', 'Psat6g221800' => 'psa', 'Psat7g065880' => 'psa', 'PSO063G5077' => 'pso', 'PSO063G6007' => 'pso', 'PSO135G0182' => 'pso', 'PSO170G1495' => 'pso', 'PSO210G0480' => 'pso', 'PSO210G3086' => 'pso', 'PSO210G3630' => 'pso', 'PSO210G7272' => 'pso', 'PSO591G0484' => 'pso', 'PSO724G0982' => 'pso', 'PSO832G2935' => 'pso', 'PSO832G3483' => 'pso', 'QL01p002250' => 'qlo', 'QL03p025013' => 'qlo', 'QL05p065109' => 'qlo', 'QL07p011181' => 'qlo', 'RcHm_v2.0_Chr2g0112671' => 'rch', 'RcHm_v2.0_Chr3g0451421' => 'rch', 'RcHm_v2.0_Chr3g0472401' => 'rch', 'RcHm_v2.0_Chr3g0486581' => 'rch', 'RcHm_v2.0_Chr4g0414301' => 'rch', 'RcHm_v2.0_Chr4g0440871' => 'rch', 'RcHm_v2.0_Chr4g0445751' => 'rch', 'RcHm_v2.0_Chr5g0018511' => 'rch', 'RcHm_v2.0_Chr5g0020921' => 'rch', 'RcHm_v2.0_Chr7g0196901' => 'rch', 'Rhsim05G0161100' => 'rsi', 'Rhsim09G0100800' => 'rsi', 'Sabra05G0045700' => 'sbr', 'Sabra06G0026800' => 'sbr', 'Sabra08G0096400' => 'sbr', 'Sabra10G0085300' => 'sbr', 'Sabra11G0144300' => 'sbr', 'Sabra13G0036800' => 'sbr', 'Sabra16G0134200' => 'sbr', 'SabraUnG0002400' => 'sbr', 'SalBow8G0372' => 'sbo', 'SalBow8G0840' => 'sbo', 'SalBow8G1349' => 'sbo', 'SalBow8G3903' => 'sbo', 'SalBow8G5388' => 'sbo', 'Sc04g0005710' => 'sci', 'Sc06g0003720' => 'sci', 'Sc14g0007200' => 'sci', 'Sed0002304' => 'sed', 'Sed0008848' => 'sed', 'Sed0009091' => 'sed', 'Sed0015594' => 'sed', 'Sed0021286' => 'sed', 'SEGI_08408' => 'sgi', 'SEGI_16547' => 'sgi', 'SGA_v2.0_scaffold12G05982' => 'sas', 'SGA_v2.0_scaffold14G06933' => 'sas', 'SGA_v2.0_scaffold170G38827' => 'sas', 'SGA_v2.0_scaffold298G47639' => 'sas', 'SGA_v2.0_scaffold38G15056' => 'sas', 'SHI04808' => 'shi', 'SHI18377' => 'shi', 'SMO114G0097' => 'smo', 'SMO367G0722' => 'smo', 'Solyc01g097460.3' => 'sly', 'Solyc02g069620.4' => 'sly', 'Solyc05g008370.2' => 'sly', 'Solyc09g059710.2' => 'sly', 'Solyc09g059720.1' => 'sly', 'Sopen01g041130' => 'spe', 'Sopen02g018750' => 'spe', 'Sopen04g017870' => 'spe', 'Sopen05g004200' => 'spe', 'Sopen09g022880' => 'spe', 'Sp2g09310' => 'spa', 'Sp2g12750' => 'spa', 'Sp3g03630' => 'spa', 'Sp5g26270' => 'spa', 'TAR362G1204' => 'tar', 'TAR369G0116' => 'tar', 'TAR626G1915' => 'tar', 'TAR633G0026' => 'tar', 'TAR636G0103' => 'tar', 'TAR636G3567' => 'tar', 'THA.LOC104805059' => 'tha', 'THA.LOC104806244' => 'tha', 'THA.LOC104818637' => 'tha', 'THA.LOC104823893' => 'tha', 'THA.LOC104824150' => 'tha', 'Thecc.02G278500' => 'tca', 'Thecc.05G286600' => 'tca', 'Thecc.06G007400' => 'tca', 'Thhalv10000979m.g' => 'esa', 'Thhalv10000998m.g' => 'esa', 'Thhalv10004764m.g' => 'esa', 'Thhalv10019520m.g' => 'esa', 'Thhalv10021298m.g' => 'esa', 'TPR.G15970' => 'tpr', 'TPR.G4877' => 'tpr', 'TPR.G6999' => 'tpr', 'TWI12G0936' => 'twi', 'TWI12G1397' => 'twi', 'TWI31G1267' => 'twi', 'TWI38G0147' => 'twi', 'TWI74G0612' => 'twi', 'TWI75G1662' => 'twi', 'TWI79G1561' => 'twi', 'unitig_27.g25175' => 'ugi', 'unitig_27.g25176' => 'ugi', 'unitig_29.g31873' => 'ugi', 'unitig_29.g31874' => 'ugi', 'unitig_37.g12635' => 'ugi', 'unitig_699.g19473' => 'ugi', 'unitig_699.g19474' => 'ugi', 'unitig_699.g19530' => 'ugi', 'vmacro01048' => 'vma', 'vmacro18971' => 'vma', 'VMungo0251G0682' => 'vmu', 'VMungo0251G1885' => 'vmu', 'VMungo0540G0098' => 'vmu', 'VMungo0540G0517' => 'vmu', 'VMungo0720G2529' => 'vmu', 'Zm00001eb029080' => 'zma', 'Zm00001eb213570' => 'zma', 'Zm00001eb301210' => 'zma' ) $gf_id = 'HOM05D001299' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001299' ) $data_identifier = 'HOM05D001299' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 5, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 16, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 9, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 8, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 12, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 1, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 2, 'mbi' => (int) 5, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 8, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 12, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 2, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301210' $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